Digital twins (DTs) are increasingly utilized to monitor, manage, and optimize complex systems across various domains, including civil engineering. A core requirement for an effective DT is to act as a fast, accurate, and maintainable surrogate of its physical counterpart, the physical twin (PT). To this end, machine learning (ML) is frequently employed to (i) construct real-time DT prototypes using efficient reduced-order models (ROMs) derived from high-fidelity simulations of the PT's nominal behavior, and (ii) specialize these prototypes into DT instances by leveraging historical sensor data from the target PT. Despite the broad applicability of ML, its use in DT engineering remains largely ad hoc. Indeed, while conventional ML pipelines often train a single model for a specific task, DTs typically require multiple, task- and domain-dependent models. Thus, a more structured approach is required to design DTs. In this paper, we introduce DesCartes Builder, an open-source tool to enable the systematic engineering of ML-based pipelines for real-time DT prototypes and DT instances. The tool leverages an open and flexible visual data flow paradigm to facilitate the specification, composition, and reuse of ML models. It also integrates a library of parameterizable core operations and ML algorithms tailored for DT design. We demonstrate the effectiveness and usability of DesCartes Builder through a civil engineering use case involving the design of a real-time DT prototype to predict the plastic strain of a structure.